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- PDB-8tqg: Crystal Structure of Mtb Pks13 Thioesterase domain in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tqg | ||||||||||||
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Title | Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor X20419 | ||||||||||||
![]() | Polyketide synthase Pks13 | ||||||||||||
![]() | BIOSYNTHETIC PROTEIN / polyketide synthase / thioesterase | ||||||||||||
Function / homology | ![]() DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Krieger, I.V. / Sacchettini, J.C. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening. Authors: Krieger, I.V. / Yalamanchili, S. / Dickson, P. / Engelhart, C.A. / Zimmerman, M.D. / Wood, J. / Clary, E. / Nguyen, J. / Thornton, N. / Centrella, P.A. / Chan, B. / Cuozzo, J.W. / ...Authors: Krieger, I.V. / Yalamanchili, S. / Dickson, P. / Engelhart, C.A. / Zimmerman, M.D. / Wood, J. / Clary, E. / Nguyen, J. / Thornton, N. / Centrella, P.A. / Chan, B. / Cuozzo, J.W. / Gengenbacher, M. / Guie, M.A. / Guilinger, J.P. / Bienstock, C. / Hartl, H. / Hupp, C.D. / Jetson, R. / Satoh, T. / Yeoman, J.T.S. / Zhang, Y. / Dartois, V. / Schnappinger, D. / Keefe, A.D. / Sacchettini, J.C. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.3 KB | Display | ![]() |
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PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 732.8 KB | Display | ![]() |
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Full document | ![]() | 737.2 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tqvC ![]() 8tr4C ![]() 8tryC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 31777.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||||
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#2: Chemical | ChemComp-JR0 / Mass: 625.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H39N7O5 / Feature type: SUBJECT OF INVESTIGATION | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M TRIS-HCL, 2.0-1.8 M AMMONIUM SULFATE, 2%-5% V/V PPG P400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→66.63 Å / Num. obs: 15367 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 49.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.049 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.2→2.27 Å / Rmerge(I) obs: 2.24 / Num. unique obs: 1295 / CC1/2: 0.598 / Rpim(I) all: 0.931 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→59.29 Å
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Refine LS restraints |
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LS refinement shell |
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